noone@mail.com Analysis of Dieting study 16S data % Fri Sep 7 05:46:18 2018

(1.4.1.2.5) Plots of Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'.

Plots are shown with relation to various combinations of meta data variables and in different graphical representations. Lots of plots here.

(1.4.1.2.5.2) Iterating over all combinations of grouping variables
(1.4.1.2.5.2.1) Entire pool of samples
(1.4.1.2.5.2.2) Iterating over Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. profile sorting order
(1.4.1.2.5.2.2.1) Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. profile sorting order: GeneSelector paired test ranking
(1.4.1.2.5.2.2.2) Iterating over dodged vs faceted bars

The same data are shown in multiple combinations of graphical representations. This is the same data, but each plot highlights slightly different aspects of it. It is not likely that you will need every plot - pick only what you need.

(1.4.1.2.5.2.2.2.1) faceted plots. Iterating over orientation and, optionally, scaling
(1.4.1.2.5.2.2.2.1.1) Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.4.1.2.5.2.2.2.1.1.0) Table 158. Data table used for plots. Data for all pooled samples. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.4.1.2.5.2.2.2.1.1.0-3232807c75b.1.4.1.2.5.2.2.2.1.1.csv

.record.id feature l2fc
SB11.before.diet Bacteroidales 0.25574
SB16.before.diet Bacteroidales -0.07187
SB18.before.diet Bacteroidales 1.83826
SB28.before.diet Bacteroidales -0.07345
SB29.before.diet Bacteroidales 1.54675
SB34.before.diet Bacteroidales -0.08291
SB36.before.diet Bacteroidales 0.09319
SB39.before.diet Bacteroidales -0.40769
SB4.before.diet Bacteroidales -0.06401
SB41.before.diet Bacteroidales 0.02529
SB43.before.diet Bacteroidales 1.40234
SB44.before.diet Bacteroidales 8.07375
SB5.before.diet Bacteroidales -2.97396
SB9.before.diet Bacteroidales -3.47822
SB11.before.diet Clostridiales -0.82685
SB16.before.diet Clostridiales 0.56231
SB18.before.diet Clostridiales -4.55997
SB28.before.diet Clostridiales -2.07830
SB29.before.diet Clostridiales 5.73036
SB34.before.diet Clostridiales 0.45140
SB36.before.diet Clostridiales -1.07855
SB39.before.diet Clostridiales -0.15541
SB4.before.diet Clostridiales 2.22516
SB41.before.diet Clostridiales -0.13608
SB43.before.diet Clostridiales -3.34615
SB44.before.diet Clostridiales -2.36071
SB5.before.diet Clostridiales 2.10759
SB9.before.diet Clostridiales 1.31247
SB11.before.diet Lactobacillales -34.11297
SB16.before.diet Lactobacillales 1.30870
SB18.before.diet Lactobacillales 5.71092
SB28.before.diet Lactobacillales 35.04440
SB29.before.diet Lactobacillales -44.75939
SB34.before.diet Lactobacillales 2.34436
SB36.before.diet Lactobacillales 2.40346
SB39.before.diet Lactobacillales 4.10044
SB4.before.diet Lactobacillales -0.09638
SB41.before.diet Lactobacillales -2.89110
SB43.before.diet Lactobacillales -6.39088
SB44.before.diet Lactobacillales -38.40238
SB5.before.diet Lactobacillales 4.71936
SB9.before.diet Lactobacillales 5.73150
SB11.before.diet Erysipelotrichales -0.30112
SB16.before.diet Erysipelotrichales 4.98093
SB18.before.diet Erysipelotrichales -0.84117
SB28.before.diet Erysipelotrichales 0.26944
SB29.before.diet Erysipelotrichales -2.11130
SB34.before.diet Erysipelotrichales 2.05299
SB36.before.diet Erysipelotrichales -37.65902
SB39.before.diet Erysipelotrichales 3.15920
SB4.before.diet Erysipelotrichales 4.55270
SB41.before.diet Erysipelotrichales -2.85572
SB43.before.diet Erysipelotrichales -1.97859
SB44.before.diet Erysipelotrichales 1.99359
SB5.before.diet Erysipelotrichales 6.92235
SB9.before.diet Erysipelotrichales 8.60451
SB11.before.diet Selenomonadales 2.30649
SB16.before.diet Selenomonadales -0.27627
SB18.before.diet Selenomonadales -6.70741
SB28.before.diet Selenomonadales -2.71024
SB29.before.diet Selenomonadales 34.91631
SB34.before.diet Selenomonadales 3.82979
SB36.before.diet Selenomonadales 33.99639
SB39.before.diet Selenomonadales 1.93922
SB4.before.diet Selenomonadales 33.66048
SB41.before.diet Selenomonadales -1.93383
SB43.before.diet Selenomonadales -0.17246
SB44.before.diet Selenomonadales -5.00802
SB5.before.diet Selenomonadales 5.47656
SB9.before.diet Selenomonadales -41.04894
SB11.before.diet Enterobacteriales 1.11389
SB16.before.diet Enterobacteriales 6.06353
SB18.before.diet Enterobacteriales -35.27866
SB28.before.diet Enterobacteriales 3.54280
SB29.before.diet Enterobacteriales 0.00000
SB34.before.diet Enterobacteriales -0.97756
SB36.before.diet Enterobacteriales 0.00000
SB39.before.diet Enterobacteriales 0.00000
SB4.before.diet Enterobacteriales 0.00000
SB41.before.diet Enterobacteriales -36.34011
SB43.before.diet Enterobacteriales -4.06227
SB44.before.diet Enterobacteriales 1.82367
SB5.before.diet Enterobacteriales 10.53977
SB9.before.diet Enterobacteriales 2.81008
SB11.before.diet Burkholderiales -2.20796
SB16.before.diet Burkholderiales -2.90722
SB18.before.diet Burkholderiales -4.09266
SB28.before.diet Burkholderiales 0.00000
SB29.before.diet Burkholderiales 0.00000
SB34.before.diet Burkholderiales 0.18448
SB36.before.diet Burkholderiales 0.78049
SB39.before.diet Burkholderiales -1.95611
SB4.before.diet Burkholderiales 36.24544
SB41.before.diet Burkholderiales 30.89262
SB43.before.diet Burkholderiales 40.33816
SB44.before.diet Burkholderiales 0.00000
SB5.before.diet Burkholderiales 32.19202
SB9.before.diet Burkholderiales -2.43784
SB11.before.diet Verrucomicrobiales 3.39378
SB16.before.diet Verrucomicrobiales 0.00000
SB18.before.diet Verrucomicrobiales 0.00000
SB28.before.diet Verrucomicrobiales 0.00000
SB29.before.diet Verrucomicrobiales 0.00000
SB34.before.diet Verrucomicrobiales 0.00000
SB36.before.diet Verrucomicrobiales 0.00000
SB39.before.diet Verrucomicrobiales 42.83593
SB4.before.diet Verrucomicrobiales 0.00000
SB41.before.diet Verrucomicrobiales -5.40355
SB43.before.diet Verrucomicrobiales 32.02551
SB44.before.diet Verrucomicrobiales 0.00000
SB5.before.diet Verrucomicrobiales 0.00000
SB9.before.diet Verrucomicrobiales 0.00000
SB11.before.diet Unclassified_Bacteria 0.47645
SB16.before.diet Unclassified_Bacteria 2.74160
SB18.before.diet Unclassified_Bacteria 1.39761
SB28.before.diet Unclassified_Bacteria -1.31551
SB29.before.diet Unclassified_Bacteria 36.72367
SB34.before.diet Unclassified_Bacteria -1.74310
SB36.before.diet Unclassified_Bacteria -0.18150
SB39.before.diet Unclassified_Bacteria 1.20881
SB4.before.diet Unclassified_Bacteria 3.13767
SB41.before.diet Unclassified_Bacteria 1.01080
SB43.before.diet Unclassified_Bacteria -0.46890
SB44.before.diet Unclassified_Bacteria 0.28933
SB5.before.diet Unclassified_Bacteria -0.46197
SB9.before.diet Unclassified_Bacteria 5.13200
SB11.before.diet Unclassified_Firmicutes -2.39491
SB16.before.diet Unclassified_Firmicutes 3.33422
SB18.before.diet Unclassified_Firmicutes -3.18016
SB28.before.diet Unclassified_Firmicutes -33.77494
SB29.before.diet Unclassified_Firmicutes 34.91631
SB34.before.diet Unclassified_Firmicutes 2.47173
SB36.before.diet Unclassified_Firmicutes -36.84086
SB39.before.diet Unclassified_Firmicutes 2.87805
SB4.before.diet Unclassified_Firmicutes 34.66048
SB41.before.diet Unclassified_Firmicutes 1.63693
SB43.before.diet Unclassified_Firmicutes -3.06227
SB44.before.diet Unclassified_Firmicutes -4.34624
SB5.before.diet Unclassified_Firmicutes 4.32463
SB9.before.diet Unclassified_Firmicutes -0.93089
SB11.before.diet Rhizobiales -34.11297
SB16.before.diet Rhizobiales 0.00000
SB18.before.diet Rhizobiales -1.59886
SB28.before.diet Rhizobiales 0.00000
SB29.before.diet Rhizobiales 0.00000
SB34.before.diet Rhizobiales -1.04311
SB36.before.diet Rhizobiales -0.36207
SB39.before.diet Rhizobiales -0.02995
SB4.before.diet Rhizobiales 1.55271
SB41.before.diet Rhizobiales 1.57487
SB43.before.diet Rhizobiales -3.12786
SB44.before.diet Rhizobiales 0.00000
SB5.before.diet Rhizobiales 1.61414
SB9.before.diet Rhizobiales 2.22512

(1.4.1.2.5.2.2.2.1.1.1) Widget 175. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Stacked Bar Chart. Data for all pooled samples. Click to see HTML widget file in full window: ./1.4.1.2.5.2.2.2.1.1.1-3234cd5fb08Dynamic.Pivot.Table.html

(1.4.1.2.5.2.2.2.1.1.1) Widget 176. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Table Barchart. Data for all pooled samples. Click to see HTML widget file in full window: ./1.4.1.2.5.2.2.2.1.1.1-3231f4dc8c5Dynamic.Pivot.Table.html

(1.4.1.2.5.2.2.2.1.1.1) Table 159. Summary table. Data for all pooled samples. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.4.1.2.5.2.2.2.1.1.1-32331b19253.1.4.1.2.5.2.2.2.1.1.csv

feature mean sd median incidence
Unclassified_Bacteria 3.42478 9.759 0.74363 0.6429
Erysipelotrichales -0.94366 11.124 1.13152 0.5714
Clostridiales -0.15377 2.600 -0.14574 0.4286
Bacteroidales 0.43452 2.653 -0.01936 0.5000
Lactobacillales -4.66357 20.999 1.82653 0.5714
Unclassified_Firmicutes -0.02199 19.632 0.35302 0.5000
Selenomonadales 4.16201 19.778 0.88338 0.5000
Enterobacteriales -3.62606 14.064 0.00000 0.4286
Burkholderiales 9.07367 17.141 0.00000 0.4286
Rhizobiales -2.37914 9.242 0.00000 0.2857
Verrucomicrobiales 5.20369 13.929 0.00000 0.2143

(1.4.1.2.5.2.2.2.1.1.1) Figure 656. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data for all pooled samples. Sorting order of features is GeneSelector paired test ranking. bar_stacked plot. Image file: plots/3232f7dbbec.svg.

(1.4.1.2.5.2.2.2.1.1.1) Figure 657. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data for all pooled samples. Sorting order of features is GeneSelector paired test ranking. bar (sample median) plot. Image file: plots/323144e6916.svg.

(1.4.1.2.5.2.2.2.1.1.1) Figure 658. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data for all pooled samples. Sorting order of features is GeneSelector paired test ranking. violin plot. Image file: plots/3236644813a.svg.

(1.4.1.2.5.2.2.2.1.1.1) Figure 659. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data for all pooled samples. Sorting order of features is GeneSelector paired test ranking. boxplot plot. Image file: plots/3237ee367d8.svg.

(1.4.1.2.5.2.2.2.1.2) Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.4.1.2.5.2.2.2.1.2.1) Figure 660. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data for all pooled samples. Sorting order of features is GeneSelector paired test ranking. bar (sample median) plot. Image file: plots/323775bf91f.svg.

(1.4.1.2.5.2.2.2.1.2.1) Figure 661. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data for all pooled samples. Sorting order of features is GeneSelector paired test ranking. violin plot. Image file: plots/3236f184af9.svg.

(1.4.1.2.5.2.2.2.1.2.1) Figure 662. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data for all pooled samples. Sorting order of features is GeneSelector paired test ranking. boxplot plot. Image file: plots/3236df87c08.svg.

(1.4.1.2.5.2.3) Grouping variables Drug.Before.Diet
(1.4.1.2.5.2.4) Iterating over Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. profile sorting order
(1.4.1.2.5.2.4.1) Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. profile sorting order: GeneSelector paired test ranking
(1.4.1.2.5.2.4.2) Iterating over dodged vs faceted bars

The same data are shown in multiple combinations of graphical representations. This is the same data, but each plot highlights slightly different aspects of it. It is not likely that you will need every plot - pick only what you need.

(1.4.1.2.5.2.4.2.1) faceted plots. Iterating over orientation and, optionally, scaling
(1.4.1.2.5.2.4.2.1.1) Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.4.1.2.5.2.4.2.1.1.0) Table 160. Data table used for plots. Data grouped by Drug.Before.Diet. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.4.1.2.5.2.4.2.1.1.0-3235ef32a9.1.4.1.2.5.2.4.2.1.1.csv

.record.id Drug.Before.Diet feature l2fc
SB11.before.diet DrugBefore_NO Bacteroidales 0.25574
SB16.before.diet DrugBefore_YES Bacteroidales -0.07187
SB18.before.diet DrugBefore_NO Bacteroidales 1.83826
SB28.before.diet DrugBefore_YES Bacteroidales -0.07345
SB29.before.diet DrugBefore_YES Bacteroidales 1.54675
SB34.before.diet DrugBefore_YES Bacteroidales -0.08291
SB36.before.diet DrugBefore_YES Bacteroidales 0.09319
SB39.before.diet DrugBefore_YES Bacteroidales -0.40769
SB4.before.diet DrugBefore_YES Bacteroidales -0.06401
SB41.before.diet DrugBefore_YES Bacteroidales 0.02529
SB43.before.diet DrugBefore_YES Bacteroidales 1.40234
SB44.before.diet DrugBefore_YES Bacteroidales 8.07375
SB5.before.diet DrugBefore_NO Bacteroidales -2.97396
SB9.before.diet DrugBefore_NO Bacteroidales -3.47822
SB11.before.diet DrugBefore_NO Clostridiales -0.82685
SB16.before.diet DrugBefore_YES Clostridiales 0.56231
SB18.before.diet DrugBefore_NO Clostridiales -4.55997
SB28.before.diet DrugBefore_YES Clostridiales -2.07830
SB29.before.diet DrugBefore_YES Clostridiales 5.73036
SB34.before.diet DrugBefore_YES Clostridiales 0.45140
SB36.before.diet DrugBefore_YES Clostridiales -1.07855
SB39.before.diet DrugBefore_YES Clostridiales -0.15541
SB4.before.diet DrugBefore_YES Clostridiales 2.22516
SB41.before.diet DrugBefore_YES Clostridiales -0.13608
SB43.before.diet DrugBefore_YES Clostridiales -3.34615
SB44.before.diet DrugBefore_YES Clostridiales -2.36071
SB5.before.diet DrugBefore_NO Clostridiales 2.10759
SB9.before.diet DrugBefore_NO Clostridiales 1.31247
SB11.before.diet DrugBefore_NO Lactobacillales -34.11297
SB16.before.diet DrugBefore_YES Lactobacillales 1.30870
SB18.before.diet DrugBefore_NO Lactobacillales 5.71092
SB28.before.diet DrugBefore_YES Lactobacillales 35.04440
SB29.before.diet DrugBefore_YES Lactobacillales -44.75939
SB34.before.diet DrugBefore_YES Lactobacillales 2.34436
SB36.before.diet DrugBefore_YES Lactobacillales 2.40346
SB39.before.diet DrugBefore_YES Lactobacillales 4.10044
SB4.before.diet DrugBefore_YES Lactobacillales -0.09638
SB41.before.diet DrugBefore_YES Lactobacillales -2.89110
SB43.before.diet DrugBefore_YES Lactobacillales -6.39088
SB44.before.diet DrugBefore_YES Lactobacillales -38.40238
SB5.before.diet DrugBefore_NO Lactobacillales 4.71936
SB9.before.diet DrugBefore_NO Lactobacillales 5.73150
SB11.before.diet DrugBefore_NO Erysipelotrichales -0.30112
SB16.before.diet DrugBefore_YES Erysipelotrichales 4.98093
SB18.before.diet DrugBefore_NO Erysipelotrichales -0.84117
SB28.before.diet DrugBefore_YES Erysipelotrichales 0.26944
SB29.before.diet DrugBefore_YES Erysipelotrichales -2.11130
SB34.before.diet DrugBefore_YES Erysipelotrichales 2.05299
SB36.before.diet DrugBefore_YES Erysipelotrichales -37.65902
SB39.before.diet DrugBefore_YES Erysipelotrichales 3.15920
SB4.before.diet DrugBefore_YES Erysipelotrichales 4.55270
SB41.before.diet DrugBefore_YES Erysipelotrichales -2.85572
SB43.before.diet DrugBefore_YES Erysipelotrichales -1.97859
SB44.before.diet DrugBefore_YES Erysipelotrichales 1.99359
SB5.before.diet DrugBefore_NO Erysipelotrichales 6.92235
SB9.before.diet DrugBefore_NO Erysipelotrichales 8.60451
SB11.before.diet DrugBefore_NO Selenomonadales 2.30649
SB16.before.diet DrugBefore_YES Selenomonadales -0.27627
SB18.before.diet DrugBefore_NO Selenomonadales -6.70741
SB28.before.diet DrugBefore_YES Selenomonadales -2.71024
SB29.before.diet DrugBefore_YES Selenomonadales 34.91631
SB34.before.diet DrugBefore_YES Selenomonadales 3.82979
SB36.before.diet DrugBefore_YES Selenomonadales 33.99639
SB39.before.diet DrugBefore_YES Selenomonadales 1.93922
SB4.before.diet DrugBefore_YES Selenomonadales 33.66048
SB41.before.diet DrugBefore_YES Selenomonadales -1.93383
SB43.before.diet DrugBefore_YES Selenomonadales -0.17246
SB44.before.diet DrugBefore_YES Selenomonadales -5.00802
SB5.before.diet DrugBefore_NO Selenomonadales 5.47656
SB9.before.diet DrugBefore_NO Selenomonadales -41.04894
SB11.before.diet DrugBefore_NO Enterobacteriales 1.11389
SB16.before.diet DrugBefore_YES Enterobacteriales 6.06353
SB18.before.diet DrugBefore_NO Enterobacteriales -35.27866
SB28.before.diet DrugBefore_YES Enterobacteriales 3.54280
SB29.before.diet DrugBefore_YES Enterobacteriales 0.00000
SB34.before.diet DrugBefore_YES Enterobacteriales -0.97756
SB36.before.diet DrugBefore_YES Enterobacteriales 0.00000
SB39.before.diet DrugBefore_YES Enterobacteriales 0.00000
SB4.before.diet DrugBefore_YES Enterobacteriales 0.00000
SB41.before.diet DrugBefore_YES Enterobacteriales -36.34011
SB43.before.diet DrugBefore_YES Enterobacteriales -4.06227
SB44.before.diet DrugBefore_YES Enterobacteriales 1.82367
SB5.before.diet DrugBefore_NO Enterobacteriales 10.53977
SB9.before.diet DrugBefore_NO Enterobacteriales 2.81008
SB11.before.diet DrugBefore_NO Burkholderiales -2.20796
SB16.before.diet DrugBefore_YES Burkholderiales -2.90722
SB18.before.diet DrugBefore_NO Burkholderiales -4.09266
SB28.before.diet DrugBefore_YES Burkholderiales 0.00000
SB29.before.diet DrugBefore_YES Burkholderiales 0.00000
SB34.before.diet DrugBefore_YES Burkholderiales 0.18448
SB36.before.diet DrugBefore_YES Burkholderiales 0.78049
SB39.before.diet DrugBefore_YES Burkholderiales -1.95611
SB4.before.diet DrugBefore_YES Burkholderiales 36.24544
SB41.before.diet DrugBefore_YES Burkholderiales 30.89262
SB43.before.diet DrugBefore_YES Burkholderiales 40.33816
SB44.before.diet DrugBefore_YES Burkholderiales 0.00000
SB5.before.diet DrugBefore_NO Burkholderiales 32.19202
SB9.before.diet DrugBefore_NO Burkholderiales -2.43784
SB11.before.diet DrugBefore_NO Verrucomicrobiales 3.39378
SB16.before.diet DrugBefore_YES Verrucomicrobiales 0.00000
SB18.before.diet DrugBefore_NO Verrucomicrobiales 0.00000
SB28.before.diet DrugBefore_YES Verrucomicrobiales 0.00000
SB29.before.diet DrugBefore_YES Verrucomicrobiales 0.00000
SB34.before.diet DrugBefore_YES Verrucomicrobiales 0.00000
SB36.before.diet DrugBefore_YES Verrucomicrobiales 0.00000
SB39.before.diet DrugBefore_YES Verrucomicrobiales 42.83593
SB4.before.diet DrugBefore_YES Verrucomicrobiales 0.00000
SB41.before.diet DrugBefore_YES Verrucomicrobiales -5.40355
SB43.before.diet DrugBefore_YES Verrucomicrobiales 32.02551
SB44.before.diet DrugBefore_YES Verrucomicrobiales 0.00000
SB5.before.diet DrugBefore_NO Verrucomicrobiales 0.00000
SB9.before.diet DrugBefore_NO Verrucomicrobiales 0.00000
SB11.before.diet DrugBefore_NO Unclassified_Bacteria 0.47645
SB16.before.diet DrugBefore_YES Unclassified_Bacteria 2.74160
SB18.before.diet DrugBefore_NO Unclassified_Bacteria 1.39761
SB28.before.diet DrugBefore_YES Unclassified_Bacteria -1.31551
SB29.before.diet DrugBefore_YES Unclassified_Bacteria 36.72367
SB34.before.diet DrugBefore_YES Unclassified_Bacteria -1.74310
SB36.before.diet DrugBefore_YES Unclassified_Bacteria -0.18150
SB39.before.diet DrugBefore_YES Unclassified_Bacteria 1.20881
SB4.before.diet DrugBefore_YES Unclassified_Bacteria 3.13767
SB41.before.diet DrugBefore_YES Unclassified_Bacteria 1.01080
SB43.before.diet DrugBefore_YES Unclassified_Bacteria -0.46890
SB44.before.diet DrugBefore_YES Unclassified_Bacteria 0.28933
SB5.before.diet DrugBefore_NO Unclassified_Bacteria -0.46197
SB9.before.diet DrugBefore_NO Unclassified_Bacteria 5.13200
SB11.before.diet DrugBefore_NO Unclassified_Firmicutes -2.39491
SB16.before.diet DrugBefore_YES Unclassified_Firmicutes 3.33422
SB18.before.diet DrugBefore_NO Unclassified_Firmicutes -3.18016
SB28.before.diet DrugBefore_YES Unclassified_Firmicutes -33.77494
SB29.before.diet DrugBefore_YES Unclassified_Firmicutes 34.91631
SB34.before.diet DrugBefore_YES Unclassified_Firmicutes 2.47173
SB36.before.diet DrugBefore_YES Unclassified_Firmicutes -36.84086
SB39.before.diet DrugBefore_YES Unclassified_Firmicutes 2.87805
SB4.before.diet DrugBefore_YES Unclassified_Firmicutes 34.66048
SB41.before.diet DrugBefore_YES Unclassified_Firmicutes 1.63693
SB43.before.diet DrugBefore_YES Unclassified_Firmicutes -3.06227
SB44.before.diet DrugBefore_YES Unclassified_Firmicutes -4.34624
SB5.before.diet DrugBefore_NO Unclassified_Firmicutes 4.32463
SB9.before.diet DrugBefore_NO Unclassified_Firmicutes -0.93089
SB11.before.diet DrugBefore_NO Rhizobiales -34.11297
SB16.before.diet DrugBefore_YES Rhizobiales 0.00000
SB18.before.diet DrugBefore_NO Rhizobiales -1.59886
SB28.before.diet DrugBefore_YES Rhizobiales 0.00000
SB29.before.diet DrugBefore_YES Rhizobiales 0.00000
SB34.before.diet DrugBefore_YES Rhizobiales -1.04311
SB36.before.diet DrugBefore_YES Rhizobiales -0.36207
SB39.before.diet DrugBefore_YES Rhizobiales -0.02995
SB4.before.diet DrugBefore_YES Rhizobiales 1.55271
SB41.before.diet DrugBefore_YES Rhizobiales 1.57487
SB43.before.diet DrugBefore_YES Rhizobiales -3.12786
SB44.before.diet DrugBefore_YES Rhizobiales 0.00000
SB5.before.diet DrugBefore_NO Rhizobiales 1.61414
SB9.before.diet DrugBefore_NO Rhizobiales 2.22512

(1.4.1.2.5.2.4.2.1.1.1) Widget 177. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Stacked Bar Chart. Data grouped by Drug.Before.Diet. Click to see HTML widget file in full window: ./1.4.1.2.5.2.4.2.1.1.1-323710aee8aDynamic.Pivot.Table.html

(1.4.1.2.5.2.4.2.1.1.1) Widget 178. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Table Barchart. Data grouped by Drug.Before.Diet. Click to see HTML widget file in full window: ./1.4.1.2.5.2.4.2.1.1.1-32328d7c4a7Dynamic.Pivot.Table.html

(1.4.1.2.5.2.4.2.1.1.1) Table 161. Summary table. Data grouped by Drug.Before.Diet. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.4.1.2.5.2.4.2.1.1.1-32341811bba.1.4.1.2.5.2.4.2.1.1.csv

feature Drug.Before.Diet mean sd median incidence
Unclassified_Bacteria DrugBefore_NO 1.6360 2.451 0.937033 0.75
Unclassified_Bacteria DrugBefore_YES 4.1403 11.557 0.650068 0.60
Erysipelotrichales DrugBefore_NO 3.5961 4.866 3.310611 0.50
Erysipelotrichales DrugBefore_YES -2.7596 12.571 1.131517 0.60
Clostridiales DrugBefore_NO -0.4917 2.982 0.242811 0.50
Clostridiales DrugBefore_YES -0.0186 2.595 -0.145743 0.40
Bacteroidales DrugBefore_NO -1.0895 2.559 -1.359108 0.50
Bacteroidales DrugBefore_YES 1.0441 2.557 -0.019357 0.50
Lactobacillales DrugBefore_NO -4.4878 19.756 5.215139 0.75
Lactobacillales DrugBefore_YES -4.7339 22.512 0.606156 0.50
Unclassified_Firmicutes DrugBefore_NO -0.5453 3.378 -1.662897 0.25
Unclassified_Firmicutes DrugBefore_YES 0.1873 23.510 2.054333 0.60
Selenomonadales DrugBefore_NO -9.9933 21.337 -2.200460 0.50
Selenomonadales DrugBefore_YES 9.8241 16.989 0.883377 0.50
Enterobacteriales DrugBefore_NO -5.2037 20.465 1.961986 0.75
Enterobacteriales DrugBefore_YES -2.9950 12.023 0.000000 0.30
Burkholderiales DrugBefore_NO 5.8634 17.572 -2.322897 0.25
Burkholderiales DrugBefore_YES 10.3578 17.749 0.092241 0.50
Rhizobiales DrugBefore_NO -7.9681 17.510 0.007638 0.50
Rhizobiales DrugBefore_YES -0.1435 1.320 0.000000 0.20
Verrucomicrobiales DrugBefore_NO 0.8484 1.697 0.000000 0.25
Verrucomicrobiales DrugBefore_YES 6.9458 16.355 0.000000 0.20

(1.4.1.2.5.2.4.2.1.1.1) Figure 663. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. bar_stacked plot. Image file: plots/323525d3ece.svg.

(1.4.1.2.5.2.4.2.1.1.1) Figure 664. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. bar (sample median) plot. Image file: plots/3232f7b1e52.svg.

(1.4.1.2.5.2.4.2.1.1.1) Figure 665. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. violin plot. Image file: plots/32314ecd115.svg.

(1.4.1.2.5.2.4.2.1.1.1) Figure 666. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. boxplot plot. Image file: plots/3233b704a45.svg.

(1.4.1.2.5.2.4.2.1.2) Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.4.1.2.5.2.4.2.1.2.1) Figure 667. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. bar (sample median) plot. Image file: plots/3232476d345.svg.

(1.4.1.2.5.2.4.2.1.2.1) Figure 668. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. violin plot. Image file: plots/3231ff2a1a3.svg.

(1.4.1.2.5.2.4.2.1.2.1) Figure 669. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. boxplot plot. Image file: plots/323c83ee3c.svg.

(1.4.1.2.5.2.4.2.2) dodged plots. Iterating over orientation and, optionally, scaling
(1.4.1.2.5.2.4.2.2.1) Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.4.1.2.5.2.4.2.2.1.1) Figure 670. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. bar (sample median) plot. Image file: plots/3236c168e5e.svg.

(1.4.1.2.5.2.4.2.2.1.1) Figure 671. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. violin plot. Image file: plots/3232321c8ac.svg.

(1.4.1.2.5.2.4.2.2.1.1) Figure 672. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. boxplot plot. Image file: plots/323457948d7.svg.

(1.4.1.2.5.2.4.2.2.2) Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.4.1.2.5.2.4.2.2.2.1) Figure 673. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. bar (sample median) plot. Image file: plots/32392900c2.svg.

(1.4.1.2.5.2.4.2.2.2.1) Figure 674. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. violin plot. Image file: plots/3233aee936e.svg.

(1.4.1.2.5.2.4.2.2.2.1) Figure 675. Log2 fold change in abundance between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. boxplot plot. Image file: plots/32375ea4aa6.svg.

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